Ex Parte Yamada et al

Patent Trial and Appeal Board

Dec 7, 2017

12541008 (P.T.A.B. Dec. 7, 2017)

United States Patent and Trademark Office
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O.Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
12/541,008 08/13/2009 N. ALICE YAMADA 20090226-01 2472
22878 7590
Agilent Technologies, Inc.
Global IP Operations
5301 Stevens Creek Blvd
Santa Clara, CA 95051
EXAMINER
SISSON, BRADLEY L
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
12/11/2017 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
IPOPS .LEGAL @ agilent.com
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PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte N. ALICE YAMADA and PETER TSANG
Appeal 2016-000485
Application 12/541,008
Technology Center 1600
Before JEFFREY N. FREDMAN, ULRIKE W. JENKS, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal1 under 35U.S.C. § 134 involving claims to a
computer-implemented method for providing a set of FISH probe
oligonucleotide sequences. The Examiner rejected the claims as directed to
non-statutory subject matter. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm but designate our affirmance as a New Grounds of Rejection.
Statement of the Case
Background
“Fluorescence in situ hybridization (FISH). . . allows for the
detection of the presence or absence of specific DNA sequences on
chromosomes by using fluorescent probes that bind to only those parts of the
1 Appellants identify the Real Party in Interest as Agilent Technologies, Inc.
(see App. Br. 3).
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Application 12/541,008
chromosome with which they show a high degree of complementarity”
(Spec. 1:27—30). However, “since [these] probes are generated from large
pieces of DNA,” FISH has “limited resolution.” (Spec. 2:1—3.) And
“[bjecause these probes are generated over very large regions of the genome,
microtranslocations and microinversions cannot be resolved by current
method” (Spec. 2:3—5). “Thus, there has been an increasing need to
understand more subtle chromosomal defects with substantially improved
resolution, and without a priori knowledge of their location” (Spec. 2:8—10).
The Claims
Claims 1, 3, 4, 21, and 22 are on appeal. Independent claim 1 is
representative and reads as follows:
1. A computer-implemented method for providing a set of
FISH probe oligonucleotide sequences, said method
comprising:
(a) providing a plurality of overlapping tiled candidate
fluorescence in situ hybridization (FISH) probe oligonucleotide
sequences, wherein said overlapping tiled candidate FISH
probe oligonucleotide sequences are complementary to
non-repeat sequences of a genome of interest and are
preselected based on at least one probe property;
(b) sorting said plurality of overlapping tiled candidate
FISH probe oligonucleotide sequences from smallest genomic
distance to largest genomic distance between neighboring
overlapping tiled candidate FISH probe oligonucleotide
sequences to produce a sorted plurality of overlapping tiled
candidate FISH probe oligonucleotide sequences;
(c) evaluating a probe property value for a neighboring
pair of overlapping tiled candidate FISH probe oligonucleotide
sequences from said sorted plurality to identify a first member
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Application 12/541,008
of said neighboring pair with a more desirable probe property
value than a second pair member of said neighboring pair;
(d) removing said second pair member from said
plurality;
(e) reiterating said sorting, evaluating and removing steps
at least once to produce said set of FISH probe oligonucleotide
sequences; and
(f) outputting said set of FISH probe oligonucleotide
sequences, wherein said method is performed by a computer
that is specifically programmed to perform said method.
The Issue2
The Examiner rejected claims 1, 3, 4, 21, and 22 under 35 U.S.C.
§ 101 as being directed to non-statutory subject matter (Ans. 4—8).
The Examiner finds all of the claims on appeal under 35 U.S.C. § 101
as being directed to patent-ineligible subject matter because the “claim
elements both individually and in combination, do not amount to
significantly more than an abstract idea” (Ans. 6). The Examiner finds the
claims directed to “abstract ideas” combined with “recitation of generic
computer structure that serves to perform generic computer functions that
are well-understood, routine, and conventional activities” {id. at 7). The
Examiner reached this conclusion by applying the test set out in Mayo
Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66 (2012)
(Ans. 5—6) based on the two-step Alice framework. Alice Corp. Pty. Ltd. v.
CLSBanklnt’l, 134 S. Ct. 2347, 2355 (2014).
2 We note that the Examiner has withdrawn rejections under 35 U.S.C. §
112(b), 35 U.S.C. § 101 utility, 35 U.S.C. § 112(a), and 35 U.S.C. § 103(a)
{see Ans. 3).
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Appellants “submit that the subject claims are not directed to a patent
ineligible abstract idea and clearly do not seek to tie up any fundamental
truth/principle or building block of human ingenuity” (App. Br. 5).
Appellants contend the “subject method of providing a set of oligonucleotide
sequences is a method of designing FISH probes that may be used to detect
chromosomal abnormalities related to cancer, aneuploidy and the like.
Therefore, it is clear that the claimed methods are drawn to ‘improvements
to another technology or technical field’” (id.). Appellants contend the
“FISH probe sequences that are recited in the claims and that are
complementary to non-repeat sequences of a genome of interest are a
representation of the oligonucleotide molecule that have the sequence of
nucleotides specified by the FISH probe sequence” (id. at 6).
Appellants also contend
the claims recite meaningful limitations that apply the abstract
idea to probe design for FISH assays. . . . The specification
shows, e.g., in the Example section, that the design of
overlapping FISH probes results in improved FISH signals
compared to signals obtained from end-to-end tiled probes.
Thus, the specification of overlapping tiled FISH probe
sequences is a meaningful limitation to the claimed method.
(App. Br. 6).
To determine whether a claim is invalid under § 101, we employ the
two-step Alice framework. In step one, we ask whether the claims are
directed to a patent ineligible concept, such as an abstract idea or law of
nature. Alice, 134 S.Ct. at 2355; Mayo, 566 U.S. at 75—77; Ariosa
Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1375 (Fed. Cir. 2015).
While method claims are generally eligible subject matter, method claims
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that are directed only to natural phenomena are directed to a patent ineligible
concept. Ariosa, 788 F.3d at 1376.
Alice Step One
Claim 1 of the instant application is directed to a multistep process of
sorting oligonucleotide probe sequences into a desirable set that specifically
bind target sequences. That process is directed to both a law of nature and
an abstract idea. In particular, the law of nature/natural phenomenon is the
probe set. A probe “refers to a polynucleotide which can specifically
hybridize to a target polynucleotide” (Spec. 12:9—10). That function of
specific hybridization is a consequence of a natural process, i.e., it results
from a high degree of complementarity.
In addition, the recited steps of sorting, evaluating, and removing and
outputting a desired set involve categorizing and/or analyzing information.
Our reviewing Court has explained that “[information as such is an
intangible” and “that collecting information, including when limited to
particular content (which does not change its character as information),”
analyzing it, and presenting the results of the collection and analysis without
more are patent ineligible abstract concepts. See, e.g, Electric Power Group,
LLCv. Alstom S.A., 830 F.3d 1350, 1353-54 (Fed. Cir. 2016).
The claimed invention therefore is drawn to using a computer to
obtain desirable oligonucleotide probe sets that specifically bind target
sequences using known, prior art standard computer processes, a relationship
that is a patent-ineligible abstract idea. Mayo, 566 U.S. at 77.
Because the claims are directed to an abstract idea/natural law, we
turn to the second step of the Alice framework.
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Alice Step Two
In Alice step two, we examine the elements of the claims to determine
whether they contain an inventive concept sufficient to transform the
claimed naturally occurring phenomena into a patent-eligible application.
Mayo, 566 U.S. at 71—72 (quoting Alice, 134 S.Ct. at 2355). We must
consider the elements of the claims both individually and as an ordered
combination to determine whether additional elements transform the nature
of the claims into a patent-eligible concept. Ariosa, 788 F.3d at 1375.
The Specification teaches prior art methods for the first step of
providing probes “complementary to non-repeat sequences” include “a
process called RepeatMasking ... In certain embodiments, a repeat masking
tool called WindowMasker may be used to mask repetitive sequences.
WindowMasker is well known in literature” (Spec. 19:23—27).
The Specification also teaches that analysis of oligonucleotides for
probe property values was known in the prior art, teaching that the
parameters of “length, melting temperature (Tm), non-homology with other
regions of the genome, hybridization signal intensities, kinetic properties
under hybridization conditions” were disclosed in “U.S. Patent No.
6,251,588” (see Spec. 20:1-3).
The steps of sorting, removing (eliminating), reiterating, and
outputting data about oligonucleotide information are also found in the prior
art. Bondarenko,3 cited by the Examiner in the withdrawn obviousness
rejection, teaches “software tools for filtering and sorting GeneChip® array
data” (Bondarenko 3:50-51). Bondarenko teaches: “There are software
3 Bondarenko, A., US 7,269,517 B2, issued Sept. 11, 2007.
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tools available in the art for storing and manipulating data derived from
various experiments in biotechnology, or for performing some statistical
analysis of the data” (Bondarenko 3:25—28).
The steps in the “claims (e.g., arranging, storing, retrieving, sorting,
eliminating, determining) are conventional, routine, and well-known. They
involve the normal, basic functions of a computer.” Versata Development
Group, Inc. v. SAP America, Inc., 793 F.3d 1306, 1335 (Fed. Cir. 2015). “In
order for the addition of a machine to impose a meaningful limit on the
scope of a claim, it must play a significant part in permitting the claimed
method to be performed, rather than function solely as an obvious
mechanism for permitting a solution to be achieved more quickly, i.e.,
through the utilization of a computer for performing calculations.” SiRF
Tech., Inc. v. Int’l Trade Comm’n, 601 F.3d 1319, 1333 (Fed.Cir. 2010).
We conclude that the practice of the method claims does not result in
an inventive concept that transforms the abstract idea/natural phenomena of
obtaining desirable oligonucleotide probe sets that specifically bind target
sequences into a patentable invention. Mayo and Ariosa make clear that
transforming claims that are directed to a law of nature requires more than
simply stating the law of nature while adding the words “apply it.” Mayo,
566 U.S. at 72; Ariosa, 788 F.3d at 1377.
In Ariosa, the challenged claims involved a method that was a general
instruction to doctors to apply routine, conventional techniques when
seeking to detect paternally inherited cell-free fetal DNA in the blood serum
of a pregnant woman. Ariosa, 788 F.3d at 1377. The same is true here. The
claims contain steps that require using a computer to obtain non-repeat
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sequences using known techniques and evaluating those sequences based on
standard, well-known probe properties to identify desirable probes.
Appellants cannot purport to have invented providing non-repeat sequences
(see Spec. 19:22—29), sorting nucleic acid information (see Bondarenko
3:50-51), evaluating probe properties such as melting temperature, length,
or GC content (see Spec. 20:1—9), or performing routine data manipulation
steps such as removing, repeating, and outputting data regarding
oligonucleotides. No specific element is identified as inventive in the
Specification.
Therefore, as in Cleveland Clinic, the claims identify oligonucleotide
probes based on probe property values using conventional methods and
“compare those values to predetermined or control values derived from
conventional statistical methods.” Cleveland Clinic Foundation v. True
Health Diagnostics LLC, 859 F.3d 1352, 1362 (Fed. Cir. 2017).
We find unpersuasive Appellants’ argument that “the design of
overlapping FISH probes results in improved FISH signals compared to
signals obtained from end-to-end tiled probes. Thus, the specification of
overlapping tiled FISH probe sequences is a meaningful limitation to the
claimed method” (App. Br. 6).
The particular probes’ selection from which to cull those with more
desirable properties simply represents an abstract idea embodied by a law of
nature that is further defined by the recited mathematical relationship in
claim 22, i.e., a percentage of overlap with another probe. However, a
“claim directed to an abstract idea does not automatically become eligible
merely by adding a mathematical formula.” RecogniCorp, LLC v. Nintendo
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Application 12/541,008
Co., Ltd., 855 F.3d 1322, 1328 (Fed. Cir. 2017). The addition of the
mathematical formula determined using standard regression techniques
based on a natural correlation and changing raw data levels into calculated
data levels “simply changes the data into other forms of data [that] cannot
save [the claims].” Id. The claims, whether considered limitation-by­
limitation or as a whole, do not sufficiently transform the abstract
idea/natural phenomena of obtaining desirable oligonucleotide probe sets
that specifically bind target sequences into a patentable invention.
We also find unpersuasive, Appellants’ contention that because the
evaluating step implements a specific method of selecting an optimal set of
FISH probes from candidate probe sequences, it is a meaningful limitation
that applies any alleged abstract idea. (App. Br. 6—7). As already discussed,
these steps are routine and conventional. These claims simply call “on a
computer to do nothing that is even arguably an advance in physical
implementations of routine mental information-comparison and rule-
application processes.” SmartGene, Inc. v. Advanced Biological
Laboratories, SA, 555 Fed. Appx. 950, 955 (Fed. Cir. 2014). As our
reviewing Court in SmartGene noted, under similar circumstances, in such a
context, “the concern about preempting public use of certain kinds of
knowledge, emphasized in Mayo, is a grave one.” Id.
We therefore conclude that Supreme Court and Federal Circuit
precedent constrains us to conclude that all of the claims on appeal are
directed to patent-ineligible subject matter.
Because our reasoning differs from that of the Examiner, and because
we rely upon the Bondarenko reference and portions of the Specification that
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Application 12/541,008
were not relied upon by the Examiner in the § 101 rejection, we designate
our affirmance as a New Grounds of Rejection to provide Appellants with a
fair opportunity to respond to this new position.
SUMMARY
In summary, we affirm the rejection of claims 1, 3, 4, 21, and 22
under 35 U.S.C. § 101, as being directed to non-statutory subject matter.
We designate our affirmance as a new ground pursuant to 37 C.F.R.
§ 41.50(b). Section 41.50(b) provides “[a] new ground of rejection pursuant
to this paragraph shall not be considered final for judicial review.” Section
41.50(b) also provides:
When the Board enters such a non-final decision, the
appellant, within two months from the date of the decision,
must exercise one of the following two options with respect to
the new ground of rejection to avoid termination of the appeal
as to the rejected claims:
(1) Reopen prosecution. Submit an appropriate
amendment of the claims so rejected or new Evidence relating
to the claims so rejected, or both, and have the matter
reconsidered by the examiner, in which event the prosecution
will be remanded to the examiner. The new ground of rejection
is binding upon the examiner unless an amendment or new
Evidence not previously of Record is made which, in the
opinion of the examiner, overcomes the new ground of rejection
designated in the decision. Should the examiner reject the
claims, appellant may again appeal to the Board pursuant to this
subpart.
(2) Request rehearing. Request that the proceeding be
reheard under § 41.52 by the Board upon the same Record. The
request for rehearing must address any new ground of rejection
and state with particularity the points believed to have been
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Application 12/541,008
misapprehended or overlooked in entering the new ground of
rejection and also state all other grounds upon which rehearing
is sought.
Further guidance on responding to a new ground of rejection can
found in the Manual of Patent Examining Procedure § 1214.01.
No time period for taking any subsequent action in
connection with this appeal may be extended under 37 C.F.R. §
1.136(a).
AFFIRMED; 37 C.F.R, $ 41.50(b)